According to one embodiment, a magnetic disk device includes a first magnetic disk, a second magnetic disk, a first actuator with a first head which reads/writes data from/to the first magnetic disk, a second actuator with a second head which reads/writes data from/to the second magnetic disk, the second actuator operated independently from the first actuator, a first controller configured to retracts the first actuator at a first time, and a second controller configured to retract the second actuator at a second time which is shifted from the first time by a certain period of time.